Job ID = 6507891 SRX = SRX494976 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:06:42 prefetch.2.10.7: 1) Downloading 'SRR1198508'... 2020-06-26T14:06:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:09:26 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:09:26 prefetch.2.10.7: 1) 'SRR1198508' was downloaded successfully Read 33054504 spots for SRR1198508/SRR1198508.sra Written 33054504 spots for SRR1198508/SRR1198508.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:05 33054504 reads; of these: 33054504 (100.00%) were unpaired; of these: 682504 (2.06%) aligned 0 times 26899730 (81.38%) aligned exactly 1 time 5472270 (16.56%) aligned >1 times 97.94% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 10466280 / 32372000 = 0.3233 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:26:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:26:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:26:57: 1000000 INFO @ Fri, 26 Jun 2020 23:27:04: 2000000 INFO @ Fri, 26 Jun 2020 23:27:10: 3000000 INFO @ Fri, 26 Jun 2020 23:27:16: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:27:21: 5000000 INFO @ Fri, 26 Jun 2020 23:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:27:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:28: 6000000 INFO @ Fri, 26 Jun 2020 23:27:29: 1000000 INFO @ Fri, 26 Jun 2020 23:27:35: 7000000 INFO @ Fri, 26 Jun 2020 23:27:37: 2000000 INFO @ Fri, 26 Jun 2020 23:27:42: 8000000 INFO @ Fri, 26 Jun 2020 23:27:45: 3000000 INFO @ Fri, 26 Jun 2020 23:27:49: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:27:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:52: 4000000 INFO @ Fri, 26 Jun 2020 23:27:56: 10000000 INFO @ Fri, 26 Jun 2020 23:27:58: 1000000 INFO @ Fri, 26 Jun 2020 23:28:00: 5000000 INFO @ Fri, 26 Jun 2020 23:28:03: 11000000 INFO @ Fri, 26 Jun 2020 23:28:05: 2000000 INFO @ Fri, 26 Jun 2020 23:28:08: 6000000 INFO @ Fri, 26 Jun 2020 23:28:10: 12000000 INFO @ Fri, 26 Jun 2020 23:28:13: 3000000 INFO @ Fri, 26 Jun 2020 23:28:15: 7000000 INFO @ Fri, 26 Jun 2020 23:28:18: 13000000 INFO @ Fri, 26 Jun 2020 23:28:20: 4000000 INFO @ Fri, 26 Jun 2020 23:28:23: 8000000 INFO @ Fri, 26 Jun 2020 23:28:25: 14000000 INFO @ Fri, 26 Jun 2020 23:28:27: 5000000 INFO @ Fri, 26 Jun 2020 23:28:31: 9000000 INFO @ Fri, 26 Jun 2020 23:28:32: 15000000 INFO @ Fri, 26 Jun 2020 23:28:34: 6000000 INFO @ Fri, 26 Jun 2020 23:28:39: 10000000 INFO @ Fri, 26 Jun 2020 23:28:39: 16000000 INFO @ Fri, 26 Jun 2020 23:28:41: 7000000 INFO @ Fri, 26 Jun 2020 23:28:46: 17000000 INFO @ Fri, 26 Jun 2020 23:28:46: 11000000 INFO @ Fri, 26 Jun 2020 23:28:48: 8000000 INFO @ Fri, 26 Jun 2020 23:28:53: 18000000 INFO @ Fri, 26 Jun 2020 23:28:54: 12000000 INFO @ Fri, 26 Jun 2020 23:28:55: 9000000 INFO @ Fri, 26 Jun 2020 23:29:00: 19000000 INFO @ Fri, 26 Jun 2020 23:29:02: 13000000 INFO @ Fri, 26 Jun 2020 23:29:02: 10000000 INFO @ Fri, 26 Jun 2020 23:29:07: 20000000 INFO @ Fri, 26 Jun 2020 23:29:09: 11000000 INFO @ Fri, 26 Jun 2020 23:29:09: 14000000 INFO @ Fri, 26 Jun 2020 23:29:14: 21000000 INFO @ Fri, 26 Jun 2020 23:29:16: 12000000 INFO @ Fri, 26 Jun 2020 23:29:17: 15000000 INFO @ Fri, 26 Jun 2020 23:29:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:29:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:29:20: #1 total tags in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:29:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:29:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:29:20: #1 tags after filtering in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:29:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:29:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:29:22: #2 number of paired peaks: 161 WARNING @ Fri, 26 Jun 2020 23:29:22: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 26 Jun 2020 23:29:22: start model_add_line... INFO @ Fri, 26 Jun 2020 23:29:22: start X-correlation... INFO @ Fri, 26 Jun 2020 23:29:22: end of X-cor INFO @ Fri, 26 Jun 2020 23:29:22: #2 finished! INFO @ Fri, 26 Jun 2020 23:29:22: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:29:22: #2 alternative fragment length(s) may be 1,12,45,396,566,591 bps INFO @ Fri, 26 Jun 2020 23:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05_model.r WARNING @ Fri, 26 Jun 2020 23:29:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:29:22: #2 You may need to consider one of the other alternative d(s): 1,12,45,396,566,591 WARNING @ Fri, 26 Jun 2020 23:29:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:29:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:29:23: 13000000 INFO @ Fri, 26 Jun 2020 23:29:25: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:29:30: 14000000 INFO @ Fri, 26 Jun 2020 23:29:33: 17000000 INFO @ Fri, 26 Jun 2020 23:29:37: 15000000 INFO @ Fri, 26 Jun 2020 23:29:41: 18000000 INFO @ Fri, 26 Jun 2020 23:29:44: 16000000 INFO @ Fri, 26 Jun 2020 23:29:48: 19000000 INFO @ Fri, 26 Jun 2020 23:29:51: 17000000 INFO @ Fri, 26 Jun 2020 23:29:56: 20000000 INFO @ Fri, 26 Jun 2020 23:29:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:29:58: 18000000 INFO @ Fri, 26 Jun 2020 23:30:03: 21000000 INFO @ Fri, 26 Jun 2020 23:30:05: 19000000 INFO @ Fri, 26 Jun 2020 23:30:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:30:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:30:10: #1 total tags in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:30:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:30:11: #1 tags after filtering in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:30:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:30:11: #1 finished! INFO @ Fri, 26 Jun 2020 23:30:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:30:12: 20000000 INFO @ Fri, 26 Jun 2020 23:30:12: #2 number of paired peaks: 161 WARNING @ Fri, 26 Jun 2020 23:30:12: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 26 Jun 2020 23:30:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:30:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:30:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:30:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:30:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:30:12: #2 alternative fragment length(s) may be 1,12,45,396,566,591 bps INFO @ Fri, 26 Jun 2020 23:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10_model.r WARNING @ Fri, 26 Jun 2020 23:30:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:30:12: #2 You may need to consider one of the other alternative d(s): 1,12,45,396,566,591 WARNING @ Fri, 26 Jun 2020 23:30:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:30:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.05_summits.bed INFO @ Fri, 26 Jun 2020 23:30:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:30:18: 21000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:30:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:30:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:30:24: #1 total tags in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:30:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:30:24: #1 tags after filtering in treatment: 21905720 INFO @ Fri, 26 Jun 2020 23:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:30:24: #1 finished! INFO @ Fri, 26 Jun 2020 23:30:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:30:25: #2 number of paired peaks: 161 WARNING @ Fri, 26 Jun 2020 23:30:25: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 26 Jun 2020 23:30:25: start model_add_line... INFO @ Fri, 26 Jun 2020 23:30:26: start X-correlation... INFO @ Fri, 26 Jun 2020 23:30:26: end of X-cor INFO @ Fri, 26 Jun 2020 23:30:26: #2 finished! INFO @ Fri, 26 Jun 2020 23:30:26: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:30:26: #2 alternative fragment length(s) may be 1,12,45,396,566,591 bps INFO @ Fri, 26 Jun 2020 23:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20_model.r WARNING @ Fri, 26 Jun 2020 23:30:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:30:26: #2 You may need to consider one of the other alternative d(s): 1,12,45,396,566,591 WARNING @ Fri, 26 Jun 2020 23:30:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:30:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:30:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:31:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.10_summits.bed INFO @ Fri, 26 Jun 2020 23:31:07: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494976/SRX494976.20_summits.bed INFO @ Fri, 26 Jun 2020 23:31:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling